taxastandJoel Nitta1, Wataru Iwasaki1
1: The University of Tokyo Botany 2022
https://joelnitta.github.io/botany_2022_taxastand
Page (2013)
taxastandAvailable at https://github.com/joelnitta/taxastand
In R:
Also, need to either install taxon-tools or Docker
res <- ts_match_names(
query = "Crepidomanes minutum K. Iwats.",
reference = c(
"Crepidomanes minutum (Bl.) K. Iwats.",
"Hymenophyllum polyanthos (Sw.) Sw."),
simple = TRUE,
docker = TRUE
)
glimpse(res)Rows: 1
Columns: 3
$ query <chr> "Crepidomanes minutum K. Iwats."
$ reference <chr> "Crepidomanes minutum (Bl.) K. Iwats."
$ match_type <chr> "auto_basio-"
data(filmy_taxonomy)
head(filmy_taxonomy[c("taxonID", "acceptedNameUsageID",
"taxonomicStatus", "scientificName")]) taxonID acceptedNameUsageID taxonomicStatus
1 54115096 NA accepted name
2 54133783 54115097 synonym
3 54115097 NA accepted name
4 54133784 54115098 synonym
5 54115098 NA accepted name
6 54133785 54115099 synonym
scientificName
1 Cephalomanes atrovirens Presl
2 Trichomanes crassum Copel.
3 Cephalomanes crassum (Copel.) M. G. Price
4 Trichomanes densinervium Copel.
5 Cephalomanes densinervium (Copel.) Copel.
6 Trichomanes infundibulare Alderw.
Any dataframe following Darwin Core standards
taxastand)Download CSV, load into R with read.csv (may require some additional wrangling)
Can use dwctaxon (https://github.com/joelnitta/dwctaxon) to handle taxonomic data in compliance with Darwin Core
res <- ts_resolve_names(
query = "Gonocormus minutum",
ref_taxonomy = filmy_taxonomy,
docker = TRUE)
glimpse(res)Rows: 1
Columns: 6
$ query <chr> "Gonocormus minutum"
$ resolved_name <chr> "Crepidomanes minutum (Bl.) K. Iwats."
$ matched_name <chr> "Gonocormus minutus (Bl.) Bosch"
$ resolved_status <chr> "accepted name"
$ matched_status <chr> "synonym"
$ match_type <chr> "auto_fuzzy"
GreenList and GBIF do not use the same taxonomy.
Of 1,092 species (331,453 occurrences) in GBIF data,
770 names resolved (302,985 occurrences) to names in Green List
| Match type | n |
|---|---|
| Full match | 516 |
| Difference in punctuation | 196 |
| Missing author | 22 |
| Taxonomic rule | 20 |
| Fuzzy match | 16 |
| TOTAL | 770 |
taxastand allows for reliable, customizable taxonomic resolutionPlease choose the tool that works best for you!
(see Grenié et al. 2022)